Luis, Thanks a lot!
I just realize that the xml file from TPP output is already run through PeptideProphet with 0.05 cutoff. I will try to rerun the xtandem along to see how it works. Best, Ping On Apr 16, 11:52 am, Luis Mendoza <[email protected]> wrote: > Hello Ping, > Yes, please make sure you run xinteract with the -p0 (zero, not "O") > option. QualScore uses those to model the "bad" spectra. > --Luis > > On Thu, Apr 16, 2009 at 10:43 AM, Ping <[email protected]> wrote: > > > Luis, > > > I finally got my PepXMLViewer working. I opened the file, and there is > > no entries with exact zero > > probability. But there are tons of entries with ~0.05 probability. > > Does that matter? Or QualScore > > only considers that zero probability as bad spectra? > > > The data is LTQ data, and first is searched under X!tandem. The result > > I used is from TPP. > > > Thanks again! > > > Ping > > > On Apr 15, 3:42 pm, Luis Mendoza <[email protected]> wrote: > > > Hi Ping, > > > By "the same results", do you mean that all of the program output is > > > identical? (e.g. the number of spectra used, etc) Or just that you also > > get > > > an unusable training set? I would first make sure that you are setting > > the > > > -p0 option successfully by opening the PeptideProphet results in the > > PepXML > > > Viewer, and look for entries with zero probability; there should be many. > > > You can also look at the following thread for some other hints: > >http://groups.google.com/group/spctools-discuss/browse_thread/thread/.<http://groups.google.com/group/spctools-discuss/browse_thread/thread/> > > .. > > > > Otherwise the software does suggest that it cannot find any "bad" spectra > > to > > > derive a training set. What kind of instrument did you use to acquire > > your > > > data? Did you do any pre-processing before searching? > > > --Luis > > > > On Wed, Apr 15, 2009 at 1:43 PM, Ping <[email protected]> wrote: > > > > > Hi Luis, > > > > > Thanks a lot for your response. > > > > > I used the x!Tandem results, all.pep.xml + original mzXML files as > > > > input. But I got following error. > > > > > Features calculated for: 24780 (1171916 ms) > > > > Training set: 12699/0 (good/bad) > > > > Unassigned spectra: 2611 > > > > ERROR: Training set distribution unusable. > > > > > I searched the post in the group, and used -p0 option, but still I got > > > > the same results. Does that mean my original mzXML has too little low > > > > quality spectral data? > > > > > Thanks again, > > > > > Ping > > > > > On Apr 15, 11:44 am, Luis Mendoza <[email protected]> wrote: > > > > > Hello Ping, > > > > > Qualscore uses a pepXML file with *all* PeptideProphet probabilities > > > > (i.e. > > > > > P>=0.0). As such, you will first need to search your data and run it > > > > > through PeptideProphet before you can use QualScore. You can find > > more > > > > > information about the algorithm in the publication listed in the > > README > > > > > file: > > > >http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/REA. > > .. > > > > > > Best of luck, and thanks for trying out our software. > > > > > --Luis > > > > > > On Wed, Apr 15, 2009 at 10:15 AM, Ping <[email protected]> wrote: > > > > > > > Hi All, > > > > > > > I just downloaded the qualscore from sashimi, and installed it on > > my > > > > > > Ubuntu machine. The command line should be: > > > > > > > java -jar qualscore_v1.0_2.jar someXML file > > > > > > > I am not sure what this XML suppose to be look like? Can anyone > > send > > > > > > me an example of it? > > > > > > > I am a newbie in this area. So please forgive me if the question is > > > > > > too simple. > > > > > > > Thanks! > > > > > > > Ping --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
